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Evolutionary biochemistry: revealing the historical and physical causes of protein properties

Nature reviews. Genetics, 2013-08, Vol.14 (8), p.559-571

2013

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Molecular ensembles make evolution unpredictable

Proceedings of the National Academy of Sciences - PNAS, 2017-11, Vol.114 (45), p.11938-11943

2017

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High-order epistasis shapes evolutionary trajectories

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005541-e1005541

2017

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Analyzing protein structure and function using ancestral gene reconstruction

Current opinion in structural biology, 2010-06, Vol.20 (3), p.360-366

2010

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The thermostability and specificity of ancient proteins

Current opinion in structural biology, 2016-06, Vol.38, p.37-43

2016

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Thermodynamic system drift in protein evolution

PLoS biology, 2014-11, Vol.12 (11), p.e1001994-e1001994

2014

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Higher-order interactions shape microbial interactions as microbial community complexity increases

Scientific reports, 2022-12, Vol.12 (1), p.22640-22640, Article 22640

2022

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Bacterial vampirism mediated through taxis to serum

eLife, 2024-05, Vol.12

2024

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Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor

PLoS biology, 2010-10, Vol.8 (10), p.e1000497

2010

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Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty

Molecular biology and evolution, 2017-02, Vol.34 (2), p.247-261

2017

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Topiary: Pruning the manual labor from ancestral sequence reconstruction

Protein science, 2023-02, Vol.32 (2), p.e4551-n/a

2023

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Evolution of minimal specificity and promiscuity in steroid hormone receptors

PLoS genetics, 2012-11, Vol.8 (11), p.e1003072

2012

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Arginine residues at internal positions in a protein are always charged

Proceedings of the National Academy of Sciences - PNAS, 2011-11, Vol.108 (47), p.18954-18959

2011

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Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family

PloS one, 2016-10, Vol.11 (10), p.e0164740-e0164740

2016

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Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9

eLife, 2020-04, Vol.9

2020

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Inferring a complete genotype-phenotype map from a small number of measured phenotypes

PLoS computational biology, 2020-09, Vol.16 (9), p.e1008243-e1008243

2020

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Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide

Frontiers in immunology, 2018-02, Vol.9, p.304-304

2018

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Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors

Proceedings of the National Academy of Sciences - PNAS, 2013-07, Vol.110 (28), p.11475-11480

2013

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Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps

Genetics (Austin), 2017-03, Vol.205 (3), p.1079-1088

2017

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Historical contingency and its biophysical basis in glucocorticoid receptor evolution

Nature (London), 2014-08, Vol.512 (7513), p.203-207

2014

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Structural Deformations in Cucurbit[n]urils: Analysis, Host‐Guest Dependence, and Automated Ellipticity Measurements Using ElliptiCB[n]

Chemistry : a European journal, 2024-10, Vol.30 (57), p.e202401981-n/a

2024

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Enzymes emerge by upcycling

Nature chemical biology, 2018-06, Vol.14 (6), p.526-527

Harms, Michael J.

2018

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Ensemble epistasis: thermodynamic origins of nonadditivity between mutations

Genetics (Austin), 2021-08, Vol.219 (1)

2021

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The importance of input sequence set to consensus‐derived proteins and their relationship to reconstructed ancestral proteins

Protein science, 2024-06, Vol.33 (6), p.e5011-n/a

2024

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Were Ancestral Proteins Less Specific?

Molecular biology and evolution, 2021-05, Vol.38 (6), p.2227-2239

2021

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Evolutionary biochemistry: revealing the historical and physical causes of protein properties

Molecular ensembles make evolution unpredictable

High-order epistasis shapes evolutionary trajectories

Analyzing protein structure and function using ancestral gene reconstruction

The thermostability and specificity of ancient proteins

Thermodynamic system drift in protein evolution

Higher-order interactions shape microbial interactions as microbial community complexity increases

Bacterial vampirism mediated through taxis to serum

Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor

Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty

Topiary: Pruning the manual labor from ancestral sequence reconstruction

Evolution of minimal specificity and promiscuity in steroid hormone receptors

Arginine residues at internal positions in a protein are always charged

Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family

Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9

Inferring a complete genotype-phenotype map from a small number of measured phenotypes

Coevolution of the Toll-Like Receptor 4 Complex with Calgranulins and Lipopolysaccharide

Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors

Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps

Historical contingency and its biophysical basis in glucocorticoid receptor evolution

Structural Deformations in Cucurbit[n]urils: Analysis, Host‐Guest Dependence, and Automated Ellipticity Measurements Using ElliptiCB[n]

Enzymes emerge by upcycling

Ensemble epistasis: thermodynamic origins of nonadditivity between mutations

The importance of input sequence set to consensus‐derived proteins and their relationship to reconstructed ancestral proteins

Were Ancestral Proteins Less Specific?

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